Average Fail Rate for Library Construction was less than 5%
3.5X coverage Clone size verification 50% paired ends BES agreement 25% of clones failed 22% need more data 3% BES disagreement Shotgun Criteria
Shotgun Complete for 12,211 Clones as of August 31st
Final Production Work 660 Clones Need Library Construction 2100 Clones In Production Pipeline Expected Completion Date December 2007
Sequence Improvement Bob Fulton Dick McCombie Rod Wing
Sequence Improvement Pipeline Shotgun_done triggers the prefinishing pipeline Initial identification of do finish regions Manual sorting and use of autoedit(Gordon) to break apart misassembly. Autofinish(Gordon) used to choose directed reactions for all gaps and regions of low quality in do finish regions Reassembly and 2nd iteration of prefinishing pipeline Final identification of do finish regions and handoff to finishing pipeline
Clone Improvement through the Prefinishing Pipeline
Improved Sequence Non-repetitve portions of the sequence have had sequence improvement (directed attempts) and have been labeled as improved. Improved regions are double stranded, sequenced with an alternate chemistry or covered by high quality data (i.e. phred quality greater than or equal to 30 or approval by an experienced finisher), unless otherwise noted. Regions of low sequence complexity (such as dinucleotide repeats and small unit tandem repeats) in the improved regions have not been resolved to previously established finishing standards. BAC end sequence, cot and methyl filtered genome survey sequence and data from overlapping projects of strain B73 may have been included in this project. Where possible, contigs have been ordered and oriented based on read pairing. These regions are designated as scaffolds. Additional order and orientation will be provided upon completion of detailed analysis of the complete finished tiling path.